I recently got a gigabit switch with support for jumbo frames, so I enabled them on the switch, and set both my vista workstation and my Debian server to a MTU of 7000.

Everything was peachy keen for a couple of days until recently I tried to access my server from the internet as opposed to over the LAN. Nothing would work. I finally narrowed it down to the recent change I made to the MTU. When I set it back to the default on the server, I could then access my webpage over the internet as well as LAN. But with it enabled I only have LAN communication. After finding this out it really was not all that surprising, but LAN worked so I assumed WAN would work as well.

My windows machine seems to be able to seamlessly transition from one to the other when it needs to. So my question is, is there any way to have this same effect in linux, where it uses jumbo frames for the LAN and regular frames for WAN requests? Or will I be forced to use two separate Ethernet cards?

Can your switch be configured so that the WAN side of the switch has a lower MTU? It sounds like there is defective software somewhere on the WAN side and instead of breaking up packets (as per the standards), the software gets very confused and simply drops the large packets. If your switch is intelligent and can handle breaking up the large packets as it sends data over the WAN, you should be fine. Otherwise you will need an intermediate router to do this job. I suspect some modem/routers (and definitely most routers) can do this breaking up for you.

Well I took your advice and thought that perhaps letting the router interfere (the server was on the DMZ) might actually help. So I forwarded port 80 and took the server off the DMZ and put the MTU back up to 7000, no dice. Although I did notice something interesting, I tried putting the MTU back down while all the static settings were set and the WAN side would still not load. So I'm now looking into that perhaps its not the MTU, but one of the static IP settings which breaks it. (Apparently you can only adjust the MTU with a static IP I've tried letting it grab the IP from the router's DHCP, but it won't keep the MTU I set, it reverts to 1500)

"but it won't keep the MTU I set, it reverts to 1500"

Perhaps the MTU is set in the DHCP negotiations? It's been years since I've read up on DHCP and I can't remember much at all.